Unclassified software tools | Small RNA sequencing data analysis

Identifies miRNA precursors (MIRs) or tasiRNA precursor (TASs) of input small RNA (sRNA). PreMIR detector is part of SoMART, the Server for plant miRNA/tasiRNA Analysis Resources and Tools. PreMIR detector identifies precursor sequences of input sRNAs and checks whether the precursor sequence can fold into the pre-miRNA structure. As input, it uses a FASTA format sRNA sequence and a selection of DNA database(s). The background program uses BLASTN to query the input sRNA sequence(s) against the selected DNA databases to find perfect matching DNA sequences, retrieves up to 200 nt flanking sequences, and reports the DNA sequence as sRNA precursor. Next it uses the UNAFold program to fold the precursor and predict the coding arms for the miRNA, and coordinates for the miRNA. If a perfect matching sequence is found that does not fold into a pre-miRNA structure, no miRNA coding arm or miRNA coordinates are predicted. Multiple sRNA FASTA sequences and multiple DNA databases can be used concurrently.

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